Starting phenix.real_space_refine on Thu May 29 10:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcj_43138/05_2025/8vcj_43138.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 116 5.49 5 Mg 7 5.21 5 S 112 5.16 5 C 20066 2.51 5 N 5771 2.21 5 O 6158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32232 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3138 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain breaks: 1 Chain: "Y" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "D" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3865 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3860 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "F" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3203 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 14, 'TRANS': 388} Chain: "G" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3142 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "X" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2523 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1029 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11863 SG CYS Y 124 20.525 82.018 113.832 1.00 70.84 S ATOM 11884 SG CYS Y 127 20.186 85.809 114.341 1.00 69.62 S ATOM 12102 SG CYS Y 152 19.509 83.328 117.286 1.00 95.98 S ATOM 28448 SG CYS X 124 55.531 58.693 57.401 1.00 76.59 S ATOM 28469 SG CYS X 127 58.085 55.831 57.789 1.00 73.57 S ATOM 28687 SG CYS X 152 58.522 58.442 54.968 1.00 98.63 S Time building chain proxies: 17.11, per 1000 atoms: 0.53 Number of scatterers: 32232 At special positions: 0 Unit cell: (183.825, 171, 192.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 116 15.00 Mg 7 11.99 O 6158 8.00 N 5771 7.00 C 20066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" ND1 HIS X 155 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 152 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 124 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 127 " pdb=" ZN Y 601 " pdb="ZN ZN Y 601 " - pdb=" NE2 HIS Y 155 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 124 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 152 " pdb="ZN ZN Y 601 " - pdb=" SG CYS Y 127 " Number of angles added : 6 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7046 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 20 sheets defined 57.5% alpha, 5.0% beta 44 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 9.39 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.580A pdb=" N ASN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.116A pdb=" N LEU A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 53 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.619A pdb=" N ARG A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 removed outlier: 4.110A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.964A pdb=" N HIS A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.587A pdb=" N SER A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.626A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.573A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.991A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.168A pdb=" N PHE A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.973A pdb=" N GLY A 287 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 3.631A pdb=" N ILE A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.669A pdb=" N TYR A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.653A pdb=" N VAL A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.714A pdb=" N ARG A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.728A pdb=" N ILE A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.544A pdb=" N LEU A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Proline residue: A 477 - end of helix removed outlier: 3.848A pdb=" N GLN A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.864A pdb=" N ALA B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.543A pdb=" N ASP B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 4.065A pdb=" N LEU B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.905A pdb=" N ASN B 95 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.527A pdb=" N HIS B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.930A pdb=" N THR B 152 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.753A pdb=" N ARG B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.507A pdb=" N ARG B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.854A pdb=" N HIS B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.054A pdb=" N PHE B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 4.250A pdb=" N PHE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.537A pdb=" N ILE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.672A pdb=" N VAL B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.619A pdb=" N LEU B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 379 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 408 through 421 Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.505A pdb=" N ARG B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 471 through 485 Proline residue: B 477 - end of helix Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.719A pdb=" N ALA C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.721A pdb=" N LEU C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.624A pdb=" N THR C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 removed outlier: 4.196A pdb=" N LEU C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 78 " --> pdb=" O GLY C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.554A pdb=" N HIS C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C 106 " --> pdb=" O GLN C 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 182 through 194 removed outlier: 4.045A pdb=" N PHE C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.224A pdb=" N ALA C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.677A pdb=" N HIS C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.230A pdb=" N MET C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.727A pdb=" N ARG C 272 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 273 " --> pdb=" O LYS C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 3.564A pdb=" N ILE C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 343 through 362 removed outlier: 3.650A pdb=" N VAL C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.545A pdb=" N LEU C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.516A pdb=" N LEU C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'Y' and resid 12 through 24 removed outlier: 3.509A pdb=" N THR Y 16 " --> pdb=" O LEU Y 12 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 37 Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.261A pdb=" N ILE Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA Y 56 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 74 removed outlier: 3.534A pdb=" N HIS Y 74 " --> pdb=" O LEU Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 84 removed outlier: 3.580A pdb=" N LEU Y 79 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA Y 81 " --> pdb=" O PRO Y 78 " (cutoff:3.500A) Proline residue: Y 82 - end of helix Processing helix chain 'Y' and resid 85 through 98 removed outlier: 4.208A pdb=" N GLU Y 97 " --> pdb=" O ILE Y 93 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 109 removed outlier: 3.797A pdb=" N HIS Y 105 " --> pdb=" O GLN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 114 Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.557A pdb=" N ALA Y 129 " --> pdb=" O PRO Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 166 through 168 No H-bonds generated for 'chain 'Y' and resid 166 through 168' Processing helix chain 'Y' and resid 189 through 200 removed outlier: 4.029A pdb=" N THR Y 193 " --> pdb=" O LEU Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 201 through 203 No H-bonds generated for 'chain 'Y' and resid 201 through 203' Processing helix chain 'Y' and resid 205 through 210 removed outlier: 3.690A pdb=" N GLN Y 209 " --> pdb=" O PRO Y 206 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU Y 210 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 230 Processing helix chain 'Y' and resid 240 through 250 Processing helix chain 'Y' and resid 251 through 258 removed outlier: 3.562A pdb=" N LYS Y 257 " --> pdb=" O GLU Y 253 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU Y 258 " --> pdb=" O ALA Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 269 through 274 Processing helix chain 'Y' and resid 283 through 295 removed outlier: 3.667A pdb=" N HIS Y 287 " --> pdb=" O SER Y 283 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Y 290 " --> pdb=" O GLN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 309 Processing helix chain 'D' and resid 29 through 35 removed outlier: 4.609A pdb=" N ASN D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.854A pdb=" N LEU D 40 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 41 " --> pdb=" O ALA D 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 41' Processing helix chain 'D' and resid 47 through 53 removed outlier: 4.352A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.505A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.535A pdb=" N LEU D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.733A pdb=" N ARG D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 196 removed outlier: 3.805A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 188 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 4.135A pdb=" N ARG D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.725A pdb=" N HIS D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.837A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 271 through 281 removed outlier: 4.086A pdb=" N PHE D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.544A pdb=" N ASN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 removed outlier: 3.921A pdb=" N TRP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.506A pdb=" N VAL D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 356 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 378 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 408 through 421 removed outlier: 3.505A pdb=" N ALA D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 Processing helix chain 'D' and resid 440 through 447 Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 471 through 484 Proline residue: D 477 - end of helix removed outlier: 3.940A pdb=" N TRP D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.502A pdb=" N TYR E 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 19 " --> pdb=" O GLU E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 19' Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.606A pdb=" N SER E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.897A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 52' Processing helix chain 'E' and resid 54 through 64 Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.948A pdb=" N LEU E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 4.285A pdb=" N ASN E 95 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 3.893A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 151 removed outlier: 3.736A pdb=" N ILE E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 removed outlier: 3.739A pdb=" N ILE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 188 " --> pdb=" O CYS E 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 209 through 224 removed outlier: 4.013A pdb=" N SER E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.639A pdb=" N HIS E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 259 removed outlier: 3.873A pdb=" N VAL E 256 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 277 removed outlier: 4.100A pdb=" N ALA E 277 " --> pdb=" O ILE E 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 305 through 317 removed outlier: 3.657A pdb=" N ILE E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 341 Processing helix chain 'E' and resid 343 through 362 removed outlier: 3.628A pdb=" N VAL E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 359 " --> pdb=" O GLN E 355 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA E 360 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 379 Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 393 through 400 Processing helix chain 'E' and resid 407 through 423 Processing helix chain 'E' and resid 429 through 435 Processing helix chain 'E' and resid 437 through 448 Processing helix chain 'E' and resid 452 through 467 Proline residue: E 458 - end of helix removed outlier: 3.947A pdb=" N LYS E 461 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 462 " --> pdb=" O PRO E 458 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 463 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 485 removed outlier: 3.588A pdb=" N LEU E 476 " --> pdb=" O ARG E 472 " (cutoff:3.500A) Proline residue: E 477 - end of helix Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 75 through 89 removed outlier: 4.137A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 80 " --> pdb=" O HIS F 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 3.880A pdb=" N HIS F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 150 removed outlier: 3.638A pdb=" N SER F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing helix chain 'F' and resid 184 through 195 removed outlier: 4.158A pdb=" N PHE F 188 " --> pdb=" O CYS F 184 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 3.818A pdb=" N ALA F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 224 removed outlier: 3.691A pdb=" N HIS F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 removed outlier: 3.732A pdb=" N HIS F 236 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 237 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER F 238 " --> pdb=" O GLN F 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 233 through 238' Processing helix chain 'F' and resid 248 through 257 removed outlier: 3.818A pdb=" N VAL F 253 " --> pdb=" O LEU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.630A pdb=" N PHE F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 286 removed outlier: 3.781A pdb=" N ARG F 284 " --> pdb=" O ARG F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 317 removed outlier: 4.030A pdb=" N ILE F 309 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 Processing helix chain 'F' and resid 343 through 362 removed outlier: 3.908A pdb=" N VAL F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 378 Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 32 through 37 removed outlier: 3.674A pdb=" N ALA G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.078A pdb=" N LEU G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN G 52 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 53 " --> pdb=" O ASP G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.735A pdb=" N ILE G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 73 through 89 removed outlier: 4.099A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.649A pdb=" N ASN G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU G 110 " --> pdb=" O GLN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 148 removed outlier: 3.652A pdb=" N ARG G 148 " --> pdb=" O THR G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.755A pdb=" N THR G 152 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 153' Processing helix chain 'G' and resid 180 through 194 removed outlier: 4.195A pdb=" N CYS G 184 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN G 186 " --> pdb=" O GLU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.824A pdb=" N SER G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.807A pdb=" N HIS G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.597A pdb=" N ARG G 239 " --> pdb=" O HIS G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 258 removed outlier: 4.123A pdb=" N GLU G 247 " --> pdb=" O GLY G 243 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET G 248 " --> pdb=" O GLY G 244 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL G 253 " --> pdb=" O LEU G 249 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL G 256 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 271 through 278 removed outlier: 3.988A pdb=" N PHE G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 317 removed outlier: 3.898A pdb=" N GLN G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 341 Processing helix chain 'G' and resid 343 through 362 removed outlier: 3.588A pdb=" N VAL G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.523A pdb=" N LEU G 379 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 392 Processing helix chain 'G' and resid 393 through 398 Processing helix chain 'X' and resid 12 through 20 removed outlier: 3.534A pdb=" N THR X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 66 through 74 Processing helix chain 'X' and resid 76 through 85 removed outlier: 4.062A pdb=" N TYR X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) Proline residue: X 82 - end of helix removed outlier: 4.061A pdb=" N GLY X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 96 removed outlier: 4.226A pdb=" N ASP X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 108 removed outlier: 4.035A pdb=" N VAL X 104 " --> pdb=" O ALA X 100 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.617A pdb=" N VAL X 128 " --> pdb=" O CYS X 124 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA X 129 " --> pdb=" O PRO X 125 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU X 130 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 168 No H-bonds generated for 'chain 'X' and resid 166 through 168' Processing helix chain 'X' and resid 176 through 181 Processing helix chain 'X' and resid 189 through 200 Processing helix chain 'X' and resid 201 through 203 No H-bonds generated for 'chain 'X' and resid 201 through 203' Processing helix chain 'X' and resid 206 through 211 removed outlier: 4.436A pdb=" N GLU X 210 " --> pdb=" O PRO X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 230 Processing helix chain 'X' and resid 240 through 250 Processing helix chain 'X' and resid 251 through 258 Processing helix chain 'X' and resid 269 through 276 Processing helix chain 'X' and resid 283 through 295 removed outlier: 3.712A pdb=" N HIS X 287 " --> pdb=" O SER X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 310 removed outlier: 3.774A pdb=" N LEU X 310 " --> pdb=" O GLN X 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.675A pdb=" N LEU A 133 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TRP A 293 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 135 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.077A pdb=" N ILE B 6 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.486A pdb=" N LEU B 132 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY B 267 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 134 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE B 291 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 133 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TRP B 293 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE B 135 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 6 through 7 removed outlier: 6.371A pdb=" N ILE C 6 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.471A pdb=" N LEU C 229 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE C 266 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 231 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 132 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLY C 267 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 134 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE C 291 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 133 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TRP C 293 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 135 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 120 through 123 removed outlier: 5.742A pdb=" N ARG Y 163 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N TYR Y 123 " --> pdb=" O PHE Y 161 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE Y 161 " --> pdb=" O TYR Y 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 232 through 233 removed outlier: 3.831A pdb=" N LYS Y 233 " --> pdb=" O HIS Y 236 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS Y 236 " --> pdb=" O LYS Y 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.996A pdb=" N LEU D 226 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 168 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET D 264 " --> pdb=" O GLY D 227 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU D 229 " --> pdb=" O MET D 264 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE D 266 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 231 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 133 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TRP D 293 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 135 " --> pdb=" O TRP D 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.534A pdb=" N ILE E 6 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 173 removed outlier: 6.623A pdb=" N ILE E 172 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 291 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 135 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP E 293 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 6 through 7 removed outlier: 6.070A pdb=" N ILE F 6 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'F' and resid 299 through 300 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.275A pdb=" N ILE G 6 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.556A pdb=" N LEU G 229 " --> pdb=" O MET G 264 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE G 266 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE G 231 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 136 " --> pdb=" O GLY G 267 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE G 291 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU G 133 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP G 293 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE G 135 " --> pdb=" O TRP G 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 120 through 121 removed outlier: 6.110A pdb=" N ARG X 163 " --> pdb=" O PHE X 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 151 through 152 1184 hydrogen bonds defined for protein. 3459 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 9.98 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10750 1.36 - 1.51: 9121 1.51 - 1.65: 13003 1.65 - 1.80: 110 1.80 - 1.95: 76 Bond restraints: 33060 Sorted by residual: bond pdb=" O3' DC H 49 " pdb=" P DG H 50 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.17e+00 bond pdb=" O3' DA H 46 " pdb=" P DG H 47 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.50e-02 4.44e+03 3.06e+00 bond pdb=" CA ILE D 457 " pdb=" CB ILE D 457 " ideal model delta sigma weight residual 1.534 1.546 -0.012 6.80e-03 2.16e+04 2.91e+00 bond pdb=" CA ILE D 457 " pdb=" C ILE D 457 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.10e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 33055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 44894 3.00 - 6.00: 310 6.00 - 9.00: 13 9.00 - 12.00: 2 12.00 - 15.00: 1 Bond angle restraints: 45220 Sorted by residual: angle pdb=" N ILE G 183 " pdb=" CA ILE G 183 " pdb=" C ILE G 183 " ideal model delta sigma weight residual 111.90 107.72 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" CA LEU D 318 " pdb=" CB LEU D 318 " pdb=" CG LEU D 318 " ideal model delta sigma weight residual 116.30 131.30 -15.00 3.50e+00 8.16e-02 1.84e+01 angle pdb=" CA GLN X 223 " pdb=" CB GLN X 223 " pdb=" CG GLN X 223 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" N GLY E 287 " pdb=" CA GLY E 287 " pdb=" C GLY E 287 " ideal model delta sigma weight residual 115.32 110.84 4.48 1.31e+00 5.83e-01 1.17e+01 angle pdb=" CB MET F 344 " pdb=" CG MET F 344 " pdb=" SD MET F 344 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 45215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 18916 35.05 - 70.11: 819 70.11 - 105.16: 37 105.16 - 140.22: 2 140.22 - 175.27: 5 Dihedral angle restraints: 19779 sinusoidal: 8871 harmonic: 10908 Sorted by residual: dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 115.27 -175.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.13 -170.13 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 103.19 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 19776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4150 0.050 - 0.099: 764 0.099 - 0.149: 172 0.149 - 0.199: 4 0.199 - 0.248: 1 Chirality restraints: 5091 Sorted by residual: chirality pdb=" CB ILE D 457 " pdb=" CA ILE D 457 " pdb=" CG1 ILE D 457 " pdb=" CG2 ILE D 457 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB VAL C 382 " pdb=" CA VAL C 382 " pdb=" CG1 VAL C 382 " pdb=" CG2 VAL C 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO F 269 " pdb=" N PRO F 269 " pdb=" C PRO F 269 " pdb=" CB PRO F 269 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 5088 not shown) Planarity restraints: 5452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS Y 124 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO Y 125 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO Y 125 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Y 125 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 405 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO E 406 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 406 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 406 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 268 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO F 269 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 269 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 269 " -0.031 5.00e-02 4.00e+02 ... (remaining 5449 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 142 2.58 - 3.16: 24569 3.16 - 3.74: 47037 3.74 - 4.32: 63281 4.32 - 4.90: 106713 Nonbonded interactions: 241742 Sorted by model distance: nonbonded pdb=" O3B ADP B 601 " pdb="MG MG B 602 " model vdw 2.002 2.170 nonbonded pdb=" OE2 GLU D 233 " pdb="MG MG D 602 " model vdw 2.010 2.170 nonbonded pdb="MG MG E 603 " pdb=" O1B ADP F 601 " model vdw 2.055 2.170 nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 2.065 2.170 nonbonded pdb=" O2G AGS C 601 " pdb="MG MG C 602 " model vdw 2.067 2.170 ... (remaining 241737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'B' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'D' and (resid 4 through 485 or resid 601 through 602)) selection = (chain 'E' and (resid 4 through 485 or resid 601 through 602)) } ncs_group { reference = (chain 'C' and resid 3 through 405) selection = (chain 'F' and (resid 3 through 278 or resid 288 through 405)) selection = (chain 'G' and resid 3 through 405) } ncs_group { reference = (chain 'X' and (resid 1 through 309 or resid 601)) selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 73.160 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33068 Z= 0.152 Angle : 0.643 15.000 45226 Z= 0.335 Chirality : 0.041 0.248 5091 Planarity : 0.004 0.066 5452 Dihedral : 17.521 175.271 12733 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 3720 helix: 0.11 (0.12), residues: 1860 sheet: 0.73 (0.35), residues: 227 loop : -1.31 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 336 HIS 0.017 0.001 HIS D 442 PHE 0.024 0.002 PHE D 311 TYR 0.025 0.001 TYR B 375 ARG 0.010 0.000 ARG E 399 Details of bonding type rmsd hydrogen bonds : bond 0.18036 ( 1296) hydrogen bonds : angle 5.70583 ( 3683) metal coordination : bond 0.00295 ( 8) metal coordination : angle 1.23178 ( 6) covalent geometry : bond 0.00340 (33060) covalent geometry : angle 0.64264 (45220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 3.179 Fit side-chains revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7541 (mttt) cc_final: 0.6604 (tptt) REVERT: Y 235 LYS cc_start: 0.6691 (ttpt) cc_final: 0.6315 (tmtt) REVERT: D 68 ASP cc_start: 0.6992 (m-30) cc_final: 0.6748 (m-30) REVERT: D 324 LYS cc_start: 0.6101 (ptmm) cc_final: 0.5068 (ptmt) REVERT: E 81 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6999 (tt0) REVERT: E 293 TRP cc_start: 0.7774 (m100) cc_final: 0.6950 (m100) REVERT: F 248 MET cc_start: 0.7145 (ptm) cc_final: 0.6632 (ptt) REVERT: F 314 ASN cc_start: 0.7825 (m110) cc_final: 0.7432 (m110) REVERT: F 344 MET cc_start: 0.7554 (mmm) cc_final: 0.7253 (mmt) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.4360 time to fit residues: 221.2504 Evaluate side-chains 256 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN Y 239 HIS D 198 ASN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 383 HIS X 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.198729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135798 restraints weight = 40462.524| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.92 r_work: 0.3406 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33068 Z= 0.154 Angle : 0.599 16.815 45226 Z= 0.303 Chirality : 0.040 0.201 5091 Planarity : 0.004 0.060 5452 Dihedral : 16.786 175.681 5335 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.92 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3720 helix: 0.33 (0.12), residues: 1895 sheet: 0.72 (0.36), residues: 204 loop : -1.34 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 336 HIS 0.014 0.001 HIS Y 239 PHE 0.015 0.001 PHE X 161 TYR 0.025 0.001 TYR D 375 ARG 0.006 0.000 ARG E 399 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1296) hydrogen bonds : angle 4.45299 ( 3683) metal coordination : bond 0.00272 ( 8) metal coordination : angle 1.49584 ( 6) covalent geometry : bond 0.00364 (33060) covalent geometry : angle 0.59868 (45220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5296 (mp) REVERT: A 206 LYS cc_start: 0.7597 (mttt) cc_final: 0.6571 (tptt) REVERT: A 344 MET cc_start: 0.8487 (mmm) cc_final: 0.8132 (mmm) REVERT: D 68 ASP cc_start: 0.7195 (m-30) cc_final: 0.6883 (m-30) REVERT: E 11 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7752 (ptm-80) REVERT: E 81 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7482 (tt0) REVERT: F 68 ASP cc_start: 0.8651 (m-30) cc_final: 0.8314 (m-30) REVERT: F 248 MET cc_start: 0.7922 (ptm) cc_final: 0.7566 (ptt) REVERT: F 314 ASN cc_start: 0.7638 (m110) cc_final: 0.7206 (m110) REVERT: F 325 ASP cc_start: 0.6811 (m-30) cc_final: 0.6435 (t0) REVERT: X 282 PHE cc_start: 0.7224 (m-80) cc_final: 0.6929 (m-80) outliers start: 30 outliers final: 20 residues processed: 302 average time/residue: 0.4422 time to fit residues: 215.3248 Evaluate side-chains 277 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 43 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 182 optimal weight: 0.0870 chunk 289 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 76 HIS E 222 ASN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 236 HIS X 10 ASN X 74 HIS X 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.195965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131369 restraints weight = 40631.213| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.88 r_work: 0.3363 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33068 Z= 0.196 Angle : 0.630 15.808 45226 Z= 0.317 Chirality : 0.041 0.191 5091 Planarity : 0.005 0.068 5452 Dihedral : 16.831 169.081 5335 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.39 % Allowed : 9.06 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3720 helix: 0.33 (0.12), residues: 1893 sheet: 0.63 (0.35), residues: 216 loop : -1.44 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 336 HIS 0.014 0.001 HIS Y 239 PHE 0.023 0.002 PHE X 161 TYR 0.025 0.002 TYR B 375 ARG 0.007 0.000 ARG E 82 Details of bonding type rmsd hydrogen bonds : bond 0.04978 ( 1296) hydrogen bonds : angle 4.34269 ( 3683) metal coordination : bond 0.00468 ( 8) metal coordination : angle 0.48981 ( 6) covalent geometry : bond 0.00479 (33060) covalent geometry : angle 0.63032 (45220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.6989 (m-30) cc_final: 0.6396 (m-30) REVERT: A 206 LYS cc_start: 0.7646 (mttt) cc_final: 0.6606 (tptt) REVERT: A 306 GLN cc_start: 0.7178 (tt0) cc_final: 0.6901 (tp-100) REVERT: A 344 MET cc_start: 0.8585 (mmm) cc_final: 0.8203 (mmm) REVERT: A 375 TYR cc_start: 0.6171 (t80) cc_final: 0.5934 (t80) REVERT: A 443 LEU cc_start: 0.7540 (mt) cc_final: 0.7322 (mt) REVERT: B 418 ASP cc_start: 0.7570 (t70) cc_final: 0.7329 (m-30) REVERT: Y 235 LYS cc_start: 0.6585 (ttpt) cc_final: 0.6129 (tmtt) REVERT: Y 291 TRP cc_start: 0.6900 (m100) cc_final: 0.6593 (m100) REVERT: D 25 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: D 68 ASP cc_start: 0.7222 (m-30) cc_final: 0.6896 (m-30) REVERT: E 11 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7730 (ptm-80) REVERT: E 81 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7537 (tt0) REVERT: F 314 ASN cc_start: 0.7641 (m110) cc_final: 0.7215 (m110) REVERT: F 344 MET cc_start: 0.8150 (tpp) cc_final: 0.7934 (mpp) REVERT: X 10 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7886 (t0) REVERT: X 282 PHE cc_start: 0.7373 (m-80) cc_final: 0.7115 (m-80) outliers start: 45 outliers final: 31 residues processed: 307 average time/residue: 0.4362 time to fit residues: 214.7971 Evaluate side-chains 292 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 10 ASN Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 215 optimal weight: 0.0870 chunk 325 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 315 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 HIS Y 239 HIS E 76 HIS F 235 GLN F 322 GLN F 341 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN X 239 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.194256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129459 restraints weight = 40628.239| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.03 r_work: 0.3363 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33068 Z= 0.182 Angle : 0.609 16.011 45226 Z= 0.306 Chirality : 0.040 0.186 5091 Planarity : 0.004 0.070 5452 Dihedral : 16.779 169.815 5335 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.69 % Allowed : 11.06 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3720 helix: 0.34 (0.12), residues: 1896 sheet: 0.51 (0.35), residues: 216 loop : -1.46 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 336 HIS 0.016 0.001 HIS Y 239 PHE 0.020 0.002 PHE X 161 TYR 0.020 0.002 TYR B 18 ARG 0.005 0.000 ARG X 247 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1296) hydrogen bonds : angle 4.27085 ( 3683) metal coordination : bond 0.00266 ( 8) metal coordination : angle 0.46103 ( 6) covalent geometry : bond 0.00445 (33060) covalent geometry : angle 0.60875 (45220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7031 (m-30) cc_final: 0.6468 (m-30) REVERT: A 206 LYS cc_start: 0.7636 (mttt) cc_final: 0.6621 (tptt) REVERT: A 344 MET cc_start: 0.8547 (mmm) cc_final: 0.8184 (mmm) REVERT: A 443 LEU cc_start: 0.7558 (mt) cc_final: 0.7341 (mt) REVERT: B 279 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6881 (tt) REVERT: Y 235 LYS cc_start: 0.6597 (ttpt) cc_final: 0.6130 (tmtt) REVERT: D 25 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: D 68 ASP cc_start: 0.7215 (m-30) cc_final: 0.6888 (m-30) REVERT: E 81 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7536 (tt0) REVERT: F 73 LEU cc_start: 0.9084 (mt) cc_final: 0.8817 (mt) REVERT: F 314 ASN cc_start: 0.7555 (m110) cc_final: 0.7156 (m110) REVERT: G 346 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7857 (mm) REVERT: X 282 PHE cc_start: 0.7452 (m-80) cc_final: 0.7171 (m-80) outliers start: 55 outliers final: 36 residues processed: 313 average time/residue: 0.4255 time to fit residues: 216.8577 Evaluate side-chains 296 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 162 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 259 optimal weight: 30.0000 chunk 375 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 349 optimal weight: 5.9990 chunk 167 optimal weight: 0.0030 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS D 383 HIS E 107 ASN E 222 ASN E 319 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN X 58 HIS X 177 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.193983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127846 restraints weight = 40531.111| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.87 r_work: 0.3352 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33068 Z= 0.182 Angle : 0.609 15.931 45226 Z= 0.306 Chirality : 0.040 0.190 5091 Planarity : 0.004 0.071 5452 Dihedral : 16.718 169.446 5335 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.03 % Allowed : 12.45 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3720 helix: 0.38 (0.12), residues: 1888 sheet: 0.36 (0.35), residues: 217 loop : -1.47 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 291 HIS 0.018 0.001 HIS Y 239 PHE 0.019 0.002 PHE X 161 TYR 0.020 0.002 TYR E 375 ARG 0.004 0.000 ARG X 247 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 1296) hydrogen bonds : angle 4.22347 ( 3683) metal coordination : bond 0.00269 ( 8) metal coordination : angle 0.46948 ( 6) covalent geometry : bond 0.00445 (33060) covalent geometry : angle 0.60921 (45220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7201 (m-30) cc_final: 0.6631 (m-30) REVERT: A 206 LYS cc_start: 0.7658 (mttt) cc_final: 0.6695 (tptt) REVERT: A 306 GLN cc_start: 0.7136 (tt0) cc_final: 0.6736 (tp-100) REVERT: A 344 MET cc_start: 0.8578 (mmm) cc_final: 0.8210 (mmm) REVERT: A 443 LEU cc_start: 0.7503 (mt) cc_final: 0.7269 (mt) REVERT: B 279 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7000 (tt) REVERT: B 418 ASP cc_start: 0.7540 (t70) cc_final: 0.7304 (m-30) REVERT: C 353 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7057 (mp) REVERT: Y 235 LYS cc_start: 0.6635 (ttpt) cc_final: 0.6155 (tmtt) REVERT: D 25 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: D 68 ASP cc_start: 0.7315 (m-30) cc_final: 0.6962 (m-30) REVERT: D 173 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: E 81 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7527 (tt0) REVERT: F 314 ASN cc_start: 0.7612 (m110) cc_final: 0.7213 (m110) REVERT: G 314 ASN cc_start: 0.8493 (m-40) cc_final: 0.8273 (m110) REVERT: G 346 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7903 (mm) REVERT: X 282 PHE cc_start: 0.7434 (m-80) cc_final: 0.7230 (m-80) outliers start: 66 outliers final: 41 residues processed: 315 average time/residue: 0.4079 time to fit residues: 209.7620 Evaluate side-chains 300 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 290 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 16 THR Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS Y 239 HIS E 319 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS G 31 GLN G 198 ASN X 177 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.196974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129827 restraints weight = 40669.666| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.82 r_work: 0.3369 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33068 Z= 0.109 Angle : 0.539 16.578 45226 Z= 0.269 Chirality : 0.038 0.154 5091 Planarity : 0.004 0.066 5452 Dihedral : 16.454 167.491 5335 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.20 % Allowed : 13.90 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3720 helix: 0.56 (0.13), residues: 1910 sheet: 0.82 (0.35), residues: 207 loop : -1.38 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 336 HIS 0.011 0.001 HIS Y 239 PHE 0.012 0.001 PHE G 120 TYR 0.017 0.001 TYR D 375 ARG 0.003 0.000 ARG X 247 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1296) hydrogen bonds : angle 4.01882 ( 3683) metal coordination : bond 0.00261 ( 8) metal coordination : angle 1.05554 ( 6) covalent geometry : bond 0.00247 (33060) covalent geometry : angle 0.53852 (45220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7127 (m-30) cc_final: 0.6572 (m-30) REVERT: A 206 LYS cc_start: 0.7513 (mttt) cc_final: 0.6614 (tptt) REVERT: A 306 GLN cc_start: 0.7117 (tt0) cc_final: 0.6721 (tp-100) REVERT: A 344 MET cc_start: 0.8549 (mmm) cc_final: 0.8237 (mmm) REVERT: A 443 LEU cc_start: 0.7454 (mt) cc_final: 0.7211 (mt) REVERT: D 25 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: D 68 ASP cc_start: 0.7259 (m-30) cc_final: 0.6883 (m-30) REVERT: E 81 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7291 (tt0) REVERT: F 252 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6328 (t80) REVERT: G 314 ASN cc_start: 0.8490 (m-40) cc_final: 0.8049 (m110) REVERT: X 282 PHE cc_start: 0.7399 (m-80) cc_final: 0.7165 (m-80) outliers start: 39 outliers final: 26 residues processed: 304 average time/residue: 0.4130 time to fit residues: 203.2197 Evaluate side-chains 289 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 124 optimal weight: 0.7980 chunk 370 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 chunk 378 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 222 ASN E 319 GLN F 107 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128372 restraints weight = 40705.438| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.77 r_work: 0.3336 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33068 Z= 0.158 Angle : 0.582 16.476 45226 Z= 0.291 Chirality : 0.039 0.177 5091 Planarity : 0.004 0.070 5452 Dihedral : 16.484 163.708 5335 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.82 % Allowed : 14.18 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3720 helix: 0.57 (0.13), residues: 1891 sheet: 0.49 (0.35), residues: 217 loop : -1.39 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 336 HIS 0.010 0.001 HIS Y 239 PHE 0.018 0.001 PHE X 161 TYR 0.019 0.001 TYR E 375 ARG 0.004 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1296) hydrogen bonds : angle 4.07333 ( 3683) metal coordination : bond 0.00249 ( 8) metal coordination : angle 0.49292 ( 6) covalent geometry : bond 0.00387 (33060) covalent geometry : angle 0.58246 (45220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7240 (m-30) cc_final: 0.6701 (m-30) REVERT: A 206 LYS cc_start: 0.7524 (mttt) cc_final: 0.6657 (tptt) REVERT: A 306 GLN cc_start: 0.7145 (tt0) cc_final: 0.6753 (tp-100) REVERT: A 344 MET cc_start: 0.8581 (mmm) cc_final: 0.8242 (mmm) REVERT: C 192 ASP cc_start: 0.8579 (p0) cc_final: 0.8355 (p0) REVERT: D 25 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: D 68 ASP cc_start: 0.7316 (m-30) cc_final: 0.6943 (m-30) REVERT: E 81 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7363 (tt0) REVERT: F 252 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6422 (t80) REVERT: G 346 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (mm) REVERT: X 282 PHE cc_start: 0.7428 (m-80) cc_final: 0.7211 (m-80) outliers start: 59 outliers final: 40 residues processed: 313 average time/residue: 0.4101 time to fit residues: 208.6723 Evaluate side-chains 305 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain Y residue 299 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 338 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 217 optimal weight: 0.0270 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 299 optimal weight: 0.8980 chunk 358 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 163 ASN E 319 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129415 restraints weight = 40551.411| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.90 r_work: 0.3345 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33068 Z= 0.121 Angle : 0.553 16.654 45226 Z= 0.275 Chirality : 0.038 0.154 5091 Planarity : 0.004 0.067 5452 Dihedral : 16.367 162.119 5335 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.73 % Allowed : 14.36 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3720 helix: 0.65 (0.13), residues: 1893 sheet: 0.63 (0.35), residues: 215 loop : -1.37 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 336 HIS 0.010 0.001 HIS D 442 PHE 0.014 0.001 PHE X 161 TYR 0.016 0.001 TYR D 375 ARG 0.007 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1296) hydrogen bonds : angle 3.99563 ( 3683) metal coordination : bond 0.00179 ( 8) metal coordination : angle 0.78256 ( 6) covalent geometry : bond 0.00282 (33060) covalent geometry : angle 0.55269 (45220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7214 (m-30) cc_final: 0.6657 (m-30) REVERT: A 165 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 206 LYS cc_start: 0.7515 (mttt) cc_final: 0.6646 (tptt) REVERT: A 306 GLN cc_start: 0.7119 (tt0) cc_final: 0.6731 (tp-100) REVERT: A 344 MET cc_start: 0.8532 (mmm) cc_final: 0.8225 (mmm) REVERT: Y 235 LYS cc_start: 0.6617 (ttpt) cc_final: 0.6122 (tmtt) REVERT: D 20 ASP cc_start: 0.7296 (m-30) cc_final: 0.6849 (t0) REVERT: D 25 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: D 68 ASP cc_start: 0.7297 (m-30) cc_final: 0.6910 (m-30) REVERT: E 81 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7327 (tt0) REVERT: E 357 ARG cc_start: 0.7016 (ttm-80) cc_final: 0.6753 (ttm-80) REVERT: F 252 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6322 (t80) REVERT: G 346 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7850 (mm) REVERT: G 364 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6277 (mt-10) REVERT: X 282 PHE cc_start: 0.7399 (m-80) cc_final: 0.7194 (m-80) outliers start: 56 outliers final: 38 residues processed: 305 average time/residue: 0.4387 time to fit residues: 218.3706 Evaluate side-chains 306 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 87 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 319 optimal weight: 3.9990 chunk 347 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 319 GLN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 HIS ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131508 restraints weight = 40341.638| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.95 r_work: 0.3388 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33068 Z= 0.127 Angle : 0.558 16.733 45226 Z= 0.277 Chirality : 0.038 0.156 5091 Planarity : 0.004 0.063 5452 Dihedral : 16.307 158.049 5335 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.69 % Allowed : 14.82 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3720 helix: 0.66 (0.13), residues: 1895 sheet: 0.60 (0.35), residues: 217 loop : -1.37 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 336 HIS 0.010 0.001 HIS D 442 PHE 0.015 0.001 PHE G 120 TYR 0.021 0.001 TYR E 375 ARG 0.007 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1296) hydrogen bonds : angle 3.99214 ( 3683) metal coordination : bond 0.00139 ( 8) metal coordination : angle 0.60872 ( 6) covalent geometry : bond 0.00301 (33060) covalent geometry : angle 0.55789 (45220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7268 (m-30) cc_final: 0.6711 (m-30) REVERT: A 206 LYS cc_start: 0.7553 (mttt) cc_final: 0.6609 (tptt) REVERT: A 306 GLN cc_start: 0.7067 (tt0) cc_final: 0.6676 (tp-100) REVERT: A 344 MET cc_start: 0.8446 (mmm) cc_final: 0.8165 (mmm) REVERT: C 353 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6854 (mp) REVERT: Y 235 LYS cc_start: 0.6621 (ttpt) cc_final: 0.6101 (tmtt) REVERT: D 20 ASP cc_start: 0.7430 (m-30) cc_final: 0.6893 (t0) REVERT: D 68 ASP cc_start: 0.7306 (m-30) cc_final: 0.6889 (m-30) REVERT: E 81 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7391 (tt0) REVERT: E 357 ARG cc_start: 0.6896 (ttm-80) cc_final: 0.6641 (ttm-80) REVERT: F 252 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6206 (t80) REVERT: G 346 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7821 (mm) REVERT: G 364 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6132 (mt-10) REVERT: X 282 PHE cc_start: 0.7522 (m-80) cc_final: 0.7310 (m-80) outliers start: 55 outliers final: 44 residues processed: 310 average time/residue: 0.4315 time to fit residues: 218.8535 Evaluate side-chains 309 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain Y residue 45 THR Chi-restraints excluded: chain Y residue 99 GLN Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 298 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 169 optimal weight: 0.0000 chunk 206 optimal weight: 0.7980 chunk 11 optimal weight: 0.0050 chunk 76 optimal weight: 0.0470 chunk 311 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 379 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS E 163 ASN E 319 GLN F 355 GLN G 198 ASN G 355 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.200822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136219 restraints weight = 40570.474| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.05 r_work: 0.3400 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33068 Z= 0.094 Angle : 0.535 20.892 45226 Z= 0.264 Chirality : 0.037 0.181 5091 Planarity : 0.004 0.063 5452 Dihedral : 16.101 161.543 5335 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 0.99 % Allowed : 15.65 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3720 helix: 0.83 (0.13), residues: 1903 sheet: 1.33 (0.35), residues: 197 loop : -1.33 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 336 HIS 0.011 0.001 HIS D 442 PHE 0.016 0.001 PHE C 120 TYR 0.017 0.001 TYR Y 123 ARG 0.007 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.02717 ( 1296) hydrogen bonds : angle 3.86255 ( 3683) metal coordination : bond 0.00436 ( 8) metal coordination : angle 1.28102 ( 6) covalent geometry : bond 0.00201 (33060) covalent geometry : angle 0.53450 (45220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7440 Ramachandran restraints generated. 3720 Oldfield, 0 Emsley, 3720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.7221 (m-30) cc_final: 0.6658 (m-30) REVERT: A 206 LYS cc_start: 0.7448 (mttt) cc_final: 0.6615 (tptt) REVERT: A 306 GLN cc_start: 0.7075 (tt0) cc_final: 0.6697 (tp-100) REVERT: A 344 MET cc_start: 0.8476 (mmm) cc_final: 0.8140 (mmm) REVERT: C 297 GLN cc_start: 0.8480 (mp10) cc_final: 0.8250 (mp10) REVERT: C 353 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6973 (mp) REVERT: Y 235 LYS cc_start: 0.6574 (ttpt) cc_final: 0.6087 (tmtt) REVERT: D 20 ASP cc_start: 0.7294 (m-30) cc_final: 0.6936 (t0) REVERT: D 68 ASP cc_start: 0.7260 (m-30) cc_final: 0.6918 (m-30) REVERT: D 148 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7707 (mmm-85) REVERT: D 320 LEU cc_start: 0.6715 (mp) cc_final: 0.6193 (pp) REVERT: E 222 ASN cc_start: 0.7786 (m-40) cc_final: 0.7573 (m110) REVERT: F 252 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6274 (t80) outliers start: 32 outliers final: 27 residues processed: 309 average time/residue: 0.4249 time to fit residues: 212.3235 Evaluate side-chains 294 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 159 VAL Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 336 TRP Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 355 GLN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain X residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 45 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 298 optimal weight: 0.0470 chunk 168 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 HIS D 319 GLN E 319 GLN F 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.198927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135104 restraints weight = 40545.522| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.81 r_work: 0.3444 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 33068 Z= 0.141 Angle : 0.643 59.155 45226 Z= 0.356 Chirality : 0.038 0.285 5091 Planarity : 0.004 0.064 5452 Dihedral : 16.102 161.599 5335 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 15.62 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3720 helix: 0.81 (0.13), residues: 1903 sheet: 1.35 (0.35), residues: 197 loop : -1.32 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 336 HIS 0.010 0.001 HIS D 442 PHE 0.018 0.001 PHE X 282 TYR 0.017 0.001 TYR Y 123 ARG 0.006 0.000 ARG F 365 Details of bonding type rmsd hydrogen bonds : bond 0.02849 ( 1296) hydrogen bonds : angle 3.86611 ( 3683) metal coordination : bond 0.00375 ( 8) metal coordination : angle 1.29237 ( 6) covalent geometry : bond 0.00311 (33060) covalent geometry : angle 0.64333 (45220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22369.67 seconds wall clock time: 385 minutes 44.73 seconds (23144.73 seconds total)